Elucidating the role of furin cleavage in SARS CoV-2 spike allostery using molecular dynamics simulations

The Coronavirus Spike glycoprotein (S) plays a key role in viral attachment, fusion and immune response; hence we must have a thorough understanding of how its dynamics drive function. A critical difference between SARS CoV-2 and its predecessors is the presence of a furin cleavage site leading to the formation of two separate subunits (S1, S2) of the Spike. The cleavage of this furin-responsive RRAR motif accelerates the post receptor-binding cascade of events by enhancing S1 shedding from S2 and is responsible for increased infectivity and transmissibility of the virus. Structural studies on the spike protein have generally been done with this motif mutated to prevent furin action, and hence the post-cleavage dynamics of the actual spike protein remain elusive. We have performed large-scale atomistic molecular dynamics simulations of this protein in the receptor-accessible (RBD-up) and the receptor-inaccessible (RBD-down) conformations, with a native glycosylation profile. To extract the essential dynamics that may drive the cleavage-triggered transitions, we performed a combined principal component analysis (PCA) on the furin-cleaved and uncleaved systems. Our findings indicate that the S1 domain of the cleaved protein undergoes a conformational ‘twist’ distinct from the intact Spike, that may be the initial trigger for the S1/S2 separation. Moreover, ‘up’ and ‘down’ orientations of the RBD actuate different ‘twist’ patterns, stipulating to provide molecular insights into the role of the receptor binding domain in this separation event. Network analysis of backbone correlated motions help us identify the most probable inter-residue pathways that drive these long-distance communications through the protein.